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Tutorials

The functionality of libSBML is difficult to capture in a single session.

Here we provide access to a number of presentations that deal with particular aspects of using libSBML together with same sample coding exercises (with answers). These are adapted versions of tutorials given in the past.

Presentations

Building and installing

This tutorial shows how to build and install libSBML.

Getting started with programming

This tutorial gives a very basic introduction to the libSBML API. It focusses on how the API relates to SBML components and attributes.

Using MIRIAM annotations

This tutorial provides information on the custom API included within libSBML that facilitates the use of MIRIAM compliant annotations.

Using MATLAB/Octave

This tutorial gives a brief introduction to building, installing and using the libSBML interface to either MATLAB and Octave.

L3 Package extensions

This tutorial deals with how to develop the plugin code that allows an SBML Level 3 package to be included with libSBML-5. It deals purely with the libSBML extension classes that register an extension and shows how to include an additional element and also an additional attrbute with a core element.

Exercises

1. Read in Model_1.xml and produce the list of reaction equations contained in the model. (i.e. information of the form: Reaction 1: A + B -> C; where A,B,C reflect the 'name' of the species - not the 'id').

Sample code

Sample C++ code

Sample Java code


2. Create a model which encodes the following:

Four parameters: p1, p2, p3 & p4

where

  • p2 = 3*p1
  • p3 = p1*p2
  • d(p4)/dt = p3/time
  • p1 = x metres
    • x is some unknown number

You will need to look at InitialAssignments/AssignmentRules/RateRules/csymbol time.

To make it slightly harder try and fully specify the units for each parameter.

Sample code

Sample C++ code

Sample Java code


Sample model

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This page was last modified 14:38, 22 April 2011.



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